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Hi
I would apply your classifier on Visium data. However, I have no clue how do it. Is there any pipeline that explain the workflow in terms of coding?
Thanks!
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Dear Professor,
Thanks for your explanation and patience! I want to know how can I find the DLPFC dataset in the tutorial:
anno_df = pd.read_csv('./data/spatialLIBD/barcode_level_layer_map.tsv',…
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Hello,
I'm interested in applying MISTy to 36 visium reactions across four timepoints. Do you have recommendations on how to implement MISTy to help identify spatially relevant features that may di…
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istar is a really nice work!
But I have the following concerning about applying istar to 10× Visium data.
① Usually, the output of 10× Visium data include a folder named spatial, which containing…
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Hi authors,
Thanks for the great work. If possible, could you share the manual annotation file for two 10X datasets with me (Figure 3A left and Figure 5A left)? Thanks!
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Hi,
I am wondering if it is possible to extract image features from a visium HD dataset using spatialdata and squidpy? Is this supported?
Thanks,
Sokratia
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While updating the Visium HD notebook I have tried converting the bins to points and plotting them, and I found that this leads to an error in `spatialdata-plot`.
Here is how to reproduce (I also c…
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- [ ] all the paths used in notebooks `00_xenium_and_visium.ipynb`, `01_xenium_and_visium.ipynb` and `02_xenium_and_visium.ipynb` should be placed in a `config.py` file
- [ ] `sandbox.zarr` was a poo…
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### Please make sure these conditions are met
- [X] I have checked that this issue has not already been reported.
- [X] I have confirmed this bug exists on the latest version of scanpy.
- [x] (option…
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Hi !
I'm trying to use CellChat to analyse multiple VISIUM datasets at once, however I doubt what should be the structure of the meta variable. Could you please let me know what should be the rown…